Flynn oversaw the handling of sexual misconduct cases from 1995 to 2008 as the leader of the Archdiocese of St. Paul and Minneapolis. An MPR News investigation found Flynn kept the Rev. Curtis Wehmeyer in ministry despite Wehmeyer's sexual addiction and sexual misconduct. Wehmeyer was eventually convicted of sexually abusing two children and possessing child pornography and is now in prison. Flynn also failed to tell police about a church investigation that found "borderline illegal" pornography on a priest's computer in 2004, and he approved extra monthly payments to priests who had admitted to sexually abusing children.

The University of St. Thomas announced Flynn's departure from the board in a news release late Saturday afternoon. It said Flynn resigned on Oct. 17 — the day of the installation of the new president of St. Thomas, Julie Sullivan.

Flynn served as board chair since 1995. His former top deputy, McDonough, had served on the board since 1991 and resigned Oct. 4. McDonough also resigned from the advisory boards for the School of Law and the Center for Catholic Studies at St. Thomas, according to the statement released Saturday.

A University spokesman said McDonough resigned from the board so that his work for the archdiocese would not be a distraction.

The board elected Michael Dougherty as interim chair and John M. Morrison as interim vice chair.
"On behalf of the Board of Trustees, I want to thank Archbishop Flynn for his many years of dedicated service to the board and to the university," Dougherty said in a statement.

The University of St. Thomas has "retained outside counsel to lead an independent investigation of matters related to clergy sexual abuse allegations that impact the university," the statement said. The board has also appointed a "special committee to oversee the investigation and to review findings and recommendations."

University president Julie Sullivan declined interview requests this week. MPR News reported Friday that the University of St. Thomas did not follow recommended restrictions on a priest and professor, the Rev. Michael Keating, who was accused of sexual abuse in 2006.

Parents of a girl who says she was sexually abused by Keating in the late 1990s notified McDonough in 2006. The archdiocese's clergy review board investigated and concluded in November 2007 that there was insufficient evidence of child sexual abuse. Nonetheless, the review board recommended to Flynn that Keating not be allowed to mentor teenagers and young adults.

Keating's teaching of young adults at the university indicates that the board's recommendation was not followed. It's unclear whether Flynn rejected the recommendation and never passed it along to the university or if university officials knew of the recommendation and disregarded it.

In a March 13, 2008 memo obtained by MPR News, McDonough told Flynn that he would inform Don Briel, the university's director of the Center for Catholic Studies, of the conclusion of the Keating investigation. "To the extent that others in the University have to be notified, we should see to that as well," McDonough wrote.

Reached at his office earlier this week, Briel wouldn't say whether he knew of the allegations.

The alleged victim sued Keating on Monday. Keating is currently on leave. He has not responded to interview requests, and his attorney, Fred Bruno, has called the abuse claims "false and highly defamatory."

The Chisago County Sheriff's Office investigated the allegations in 2006 and found insufficient evidence to file charges.